A timeline of bacterial and archaeal diversification in the ocean

Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.

Differential priority effects impact taxonomy and functionality of host-associated microbiomes

Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.

Tenacibaculum tangerinum sp. nov., isolated from a tidal flat sediment

An orange-coloured bacterium, designated as strain GRR-S3-23T, was isolated from a tidal flat sediment collected from Garorim Bay, Chuncheongbuk-do, Republic of Korea. Cells of GRR-S3-23T were aerobic, Gram-stain-negative, rod-shaped and motile. GRR-S3-23T grew at 18-40 °C (optimum, 30 °C), pH 7.0-9.0 (optimum, pH 7.0) and with 2-4 % NaCl (optimum, 2-3 % w/v). Results of 16S rRNA gene sequence analysis indicated that GRR-S3-23T was closely related to Tenacibaculum aiptasiae a4T (97.6 %), followed by Tenacibaculum aestuarii SMK-4T (97.5 %), Tenacibaculum mesophilum MBIC 1140T (97.4 %), Tenacibaculum singaporense TLL-A2T (97.3 %), Tenacibaculum crassostreae JO-1T (97.2 %),and Tenacibaculum sediminilitoris YKTF-3T (97.1 %). The average amino acid identity values between GRR-S3-23T and the related strains were 86.8-72.8 %, the average nucleotide identity values were 83.3-74.1 %, and the digital DNA-DNA hybridization values were 27.0-19.6 %. GRR-S3-23T possessed menaquinone-6 (MK-6) as major respiratory quinone and had summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 20.6 %) and iso-C15 : 1G (10.8 %) as major fatty acids (>10.0 %). The polar lipid profiles of GRR-S3-23T contained phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid, three unidentified lipids, one unidentified glycolipid and four unidentified phospholipids. The DNA G+C content of GRR-S3-23T was 33.7%. On the basis of the results of the polyphasic analysis involving phylogenetic, phylogenomic, physiological and chemotaxonomic analyses described in this study, GRR-S3-23T is considered to represent a novel species within the genus Tenacibaculum, for which the name Tenacibaculum tangerinum is proposed. The type strain is GRR-S3-23T (=KCTC 102029T=KACC 23271T=JCM 36353T).

Optimization of Siderophore Production in Three Marine Bacterial Isolates along with Their Heavy-Metal Chelation and Seed Germination Potential Determination

Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe+3) levels in surface waters in the marine environment, microbes produce a variety of siderophores. In the current study, halophilic bacteria Bacillus taeanensis SMI_1, Enterobacter sp., AABM_9, and Pseudomonas mendocina AMPPS_5 were isolated from marine surface water of Kalinga beach, Bay of Bengal (Visakhapatnam, Andhra Pradesh, India) and were investigated for siderophore production using the Chrome Azurol S (CAS) assay. The effect of various production parameters was also studied. The optimum production of siderophores for SMI_1 was 93.57% siderophore units (SU) (after 48 h of incubation at 30 °C, pH 8, sucrose as carbon source, sodium nitrate as nitrogen source, 0.4% succinic acid), and for AABM_9, it was 87.18 %SU (after 36 h of incubation period at 30 °C, pH 8, in the presence of sucrose, ammonium sulfate, 0.4% succinic acid). The maximum production of siderophores for AMPPS_5 was 91.17 %SU (after 36 h of incubation at 35 °C, pH 8.5, glucose, ammonium sulfate, 0.4% citric acid). The bacterial isolates SMI_1, AABM_9, and AMPPS_5 showed siderophore production at low Fe+3 concentrations of 0.10 µM, 0.01 µM, and 0.01 µM, respectively. The SMI_1 (73.09 %SU) and AMPPS_5 (68.26 %SU) isolates showed siderophore production in the presence of Zn+2 (10 µM), whereas AABM_9 (50.4 %SU) exhibited siderophore production in the presence of Cu+2 (10 µM). Additionally, these bacterial isolates showed better heavy-metal chelation ability and rapid development in seed germination experiments. Based on these results, the isolates of marine-derived bacteria effectively produced the maximum amount of siderophores, which could be employed in a variety of industrial and environmental applications.

Isolation and Characterization of a Serratia rubidaea from a Shallow Water Hydrothermal Vent

Microbial life present in the marine environment has to be able to adapt to rapidly changing and often extreme conditions. This makes these organisms a putative source of commercially interesting compounds since adaptation provides different biochemical routes from those found in their terrestrial counterparts. In this work, the goal was the identification of a marine bacterium isolated from a sample taken at a shallow water hydrothermal vent and of its red product. Genomic, lipidomic, and biochemical approaches were used simultaneously, and the bacterium was identified as Serratia rubidaea. A high-throughput screening strategy was used to assess the best physico-chemical conditions permitting both cell growth and production of the red product. The fatty acid composition of the microbial cells was studied to assess adaptation at the lipid level under stressful conditions, whilst several state-of-the-art techniques, such as DSC, FTIR, NMR, and Ultra-High Resolution Qq-Time-of-Flight mass spectrometry, were used to characterize the structure of the pigment. We hypothesize that the pigment, which could be produced by the cells up to 62 °C, is prodigiosin linked to an aliphatic compound that acts as an anchor to keep it close to the cells in the marine environment.

Draft genome sequences of six bacteria isolated from polylactic acid samples from the Mediterranean Sea

Here, we report the draft genome sequences of six marine strains isolated from plastic samples incubated in the Mediterranean Sea. Genomic analyses place these strains within the Alkalihalobacillus, Bacillus, Halomonas, and Marinobacter genera. Examining the genomes of these non-typical environmental bacteria increases our comprehension of microorganism biology and their potential uses.

Heavy Metal Tolerance of Microorganisms Isolated from Coastal Marine Sediments and Their Lead Removal Potential

In this study, 338 microorganisms, comprising 271 bacteria and 67 fungi, were isolated from sediment samples collected from underexplored Pacific and Caribbean regions of Colombia. Screening trials were conducted on selected strains (n = 276) to assess their tolerance to cadmium (Cd2+), lead (Pb2+), and zinc (Zn2+), leading to the identification of six bacteria capable of withstanding 750 mg·L-1 of each heavy metal ion. Three promising microorganisms, identified as Enterobacter sp. INV PRT213, Pseudomonas sp. INV PRT215, and Stenotrophomonas sp. INV PRT216 were selected for lead removal experiments using LB broth medium supplemented with 400 mg·L-1 Pb2+. Among these, Pseudomonas sp. INV PRT215 exhibited significant potential, removing 49% of initial Pb2+ after 240 min of exposure (16.7 g wet biomass·L-1, pH 5, 30 °C). Infrared spectra of Pb-exposed biomass showed changes in functional groups, including carbonyl groups of amides, carboxylate, phosphate, hydroxyl, and amine groups, compared to the not-exposed control. These changes suggested interactions between the metal and functional groups in the biomass. The findings of this study highlight the potential of microorganisms derived from coastal marine environments as promising candidates for future applications in bioremediation of polluted environments contaminated with heavy metals.

Dimethylsulfoniopropionate and its catabolites are important chemical signals mediating marine microbial interactions

Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound with key ecological roles in marine environments. This paper offers a brief insight into the mechanisms, environmental diversity, and importance of DMSP-mediated marine microbial interactions, including algae-microzooplankton interactions, bacteria-microzooplankton interactions, and algae-bacteria interactions. We also highlight current challenges that warrant further investigation.

Influence of Light Conditions on the Antibacterial Performance and Mechanism of Waterborne Fluorescent Coatings Based on Waterproof Long Afterglow Phosphors/PDMS Composites

Marine microbial adhesion is the fundamental cause of large-scale biological fouling. Low surface energy coatings can prevent marine installations from biofouling; nevertheless, their static antifouling abilities are limited in the absence of shear forces produced by seawater. Novel waterborne antifouling coatings inspired by fluorescent coral were reported in this paper. Waterproof long afterglow phosphors (WLAP) were introduced into waterborne silicone elastomers by the physical blending method. The composite coatings store energy during the day, and the various colors of light emitted at night affect the regular physiological activities of marine bacteria. Due to the synergistic effect of fouling-release and fluorescence antifouling, the WLAP/polydimethylsiloxane (PDMS) composite coating showed excellent antifouling abilities. The antibacterial performance of coatings was tested under simulated day-night alternation, continuous light, and constant dark conditions, respectively. The results illustrated that the antibacterial performance of composite coatings under simulated day-night alternation conditions was significantly better than that under continuous light or darkness. The weak lights emitted by the coating can effectively inhibit the adhesion of bacteria. C-SB/PDMS showed the best antibacterial effect, with a bacterial adhesion rate (BAR) of only 3.7%. Constant strong light also affects the normal physiological behavior of bacteria, and the weak light of coatings was covered. The antibacterial ability of coatings primarily relied on their surface properties under continuous dark conditions. The fluorescent effect played a vital role in the synergetic antifouling mechanism. This study enhanced the static antifouling abilities of coatings and provided a new direction for environmentally friendly and long-acting marine antifouling coatings.

Marine bacteria harbor the sulfonamide resistance gene sul4 without mobile genetic elements

Marine bacteria are possible reservoirs of antibiotic-resistance genes (ARGs) originating not only from clinical and terrestrial hot spots but also from the marine environment. We report here for the first time a higher rate of the sulfonamide-resistance gene sul4 in marine bacterial isolates compared with other sul genes. Among four sulfonamide-resistance genes (sul1, sul2, sul3, and sul4), sul4 was most abundant (45%) in 74 sulfonamide-resistant marine isolates by PCR screening. The order of abundance was sul4 (33 isolates) >sul2 (6 isolates) >sul3 (5 isolates) >sul1 (1 isolate). Whole-genome sequencing of 23 isolates of sul4-expressing α- and γ-proteobacteria and bacilli revealed that sul4 was not accompanied by known mobile genetic elements. This suggests that sul4 in these marine isolates is clonally transferred and not horizontally transferable. Folate metabolism genes formed a cluster with sul4, suggesting that the cluster area plays a role in folate metabolism, at which sul4 functions as a dihydropteroate synthase. Thus, sul4 might be expressed in marine species and function in folate synthesis, but it is not a transferable ARG.

A novel class of xylanases specifically degrade marine red algal β1,3/1,4-mixed-linkage xylan

Xylans are polysaccharides composed of xylose and include β1,4-xylan, β1,3-xylan, and β1,3/1,4-mixed-linkage xylan (MLX). MLX is widely present in marine red algae and constitutes a significant organic carbon in the ocean. Xylanases are hydrolase enzymes that play an important role in xylan degradation. While a variety of β1,4-xylanases and β1,3-xylanases involved in the degradation of β1,4-xylan and β1,3-xylan have been reported, no specific enzyme has yet been identified that degrades MLX. Herein, we report the characterization of a new MLX-specific xylanase from the marine bacterium Polaribacter sp. Q13 which utilizes MLX for growth. The bacterium secretes xylanases to degrade MLX, among which is Xyn26A, an MLX-specific xylanase that shows low sequence similarities (<27%) to β1,3-xylanases in the glycoside hydrolase family 26 (GH26). We show that Xyn26A attacks MLX precisely at β1,4-linkages, following a β1,3-linkage toward the reducing end. We confirm that Xyn26A and its homologs have the same specificity and mode of action on MLX, and thus represent a new xylanase group which we term as MLXases. We further solved the structure of a representative MLXase, AlXyn26A. Structural and biochemical analyses revealed that the specificity of MLXases depends critically on a precisely positioned β1,3-linkage at the -2/-1 subsite. Compared to the GH26 β1,3-xylanases, we found MLXases have evolved a tunnel-shaped cavity that is fine-tuned to specifically recognize and hydrolyze MLX. Overall, this study offers a foremost insight into MLXases, shedding light on the biochemical mechanism of bacterial degradation of MLX.

Marine Bacteria: A Source of Novel Bioactive Natural Products

Marine natural products have great pharmacological potential due to their unique and diverse chemical structures. The marine bacterial biodiversity and the unique marine environment lead to a high level of complexity and ecological interaction among marine species. This results in the production of metabolic pathways and adaptation mechanisms that are different from those of terrestrial organisms, which has drawn significant attention from researchers in the field of natural medicine. This review provides an analysis of the distribution and frequency of keywords in the literature on marine bacterial natural products as well as an overview of the new natural products isolated from the secondary metabolites of marine bacteria in recent years. Finally, it discusses the current research hotspots in this field and speculates on future directions and limitations.

Brachybacterium atlanticum sp. nov., a novel marine bacterium isolated from the Atlantic Ocean

A bacterial strain, PhyBa_CO2_2T, was isolated from the North Atlantic Gyre, offshore Terceira Island in the Azores. Initially, the NCBI nucleotide blast analysis based on 16S rRNA gene sequences revealed that the strain belongs to the genus Brachybacterium, with a 100 % identity with Brachybacterium paraconglomeratum LMG 19861T. However, further genomic characterization through average nucleotide identity (ANI) and digital DNA-DNA hybridization analyses showed values of 96.06 and 64.80 %, respectively. Comparative genomics also highlighted differences in gene content. The genome size of PhyBa_CO2_2T is 3.6 Mbp and the DNA G+C content is 72.1 mol%. Chemotaxonomic analysis demonstrated that the composition of the fatty acids was mainly composed of anteiso-C15 : 0 (46.04 %), iso-C16 : 0 (13.70 %) and anteiso-C17 : 0 (9.48 %), and the polar lipids were mainly diphosphatidylglycerol, phosphatidylglycerol and two unidentified glycolipids. Furthermore, the diagnostic amino acid of the cell wall was meso-diaminopimelic acid and the predominant menaquinone was MK7. Finally, phenotypic analysis revealed differences in biochemical profiles between PhyBa_CO2_2T and its closely related strains in terms of indole production, urease and β-glucuronidase activity. Therefore, based on the genomic, chemotaxonomic and phenotypic data obtained, we concluded that strain PhyBa_CO2_2T represents a new species, for which the name Brachybacterium atlanticum sp. nov. is proposed in reference to its isolation site. The type strain is PhyBa_CO2_2T (=DSM 114113T= CECT 30695T).

Bioprospecting for polyesterase activity relevant for PET degradation in marine Enterobacterales isolates

Plastics have quickly become an integral part of modern life. Due to excessive production and improper waste disposal, they are recognized as contaminants present in practically all habitat types. Although there are several polymers, polyethylene terephthalate (PET) is of particular concern due to its abundance in the environment. There is a need for a solution that is both cost-effective and ecologically friendly to address this pollutant. The use of microbial depolymerizing enzymes could offer a biological avenue for plastic degradation, though the full potential of these enzymes is yet to be uncovered. The purpose of this study was to use (1) plate-based screening methods to investigate the plastic degradation potential of marine bacteria from the order Enterobacterales collected from various organismal and environmental sources, and (2) perform genome-based analysis to identify polyesterases potentially related to PET degradation. 126 bacterial isolates were obtained from the strain collection of RD3, Research Unit Marine Symbioses-GEOMAR-and sequentially tested for esterase and polyesterase activity, in combination here referred to as PETase-like activity. The results show that members of the microbial families Alteromonadaceae, Shewanellaceae, and Vibrionaceae, derived from marine sponges and bryozoans, are the most promising candidates within the order Enterobacterales. Furthermore, 389 putative hydrolases from the α/β superfamily were identified in 23 analyzed genomes, of which 22 were sequenced for this study. Several candidates showed similarities with known PETases, indicating underlying enzymatic potential within the order Enterobacterales for PET degradation.

Unravelling the secrets of multi-domain lytic polysaccharide monooxygenases (LPMOs)

A new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii is described in the paper by Zhou et al. [(2023), Acta Cryst. D79, 479-497].

Evaluation of lipophosphoramidates-based amphiphilic compounds on the formation of biofilms of marine bacteria

The bacteriostatic and/or bactericidal properties of few phosphoramide-based amphiphilic compounds on human pathogenic bacteria were previously reported. In this study, the potential of two cationic (BSV36 and KLN47) and two zwitterionic (3 and 4) amphiphiles as inhibitors of marine bacterial growth and biofilm formation were investigated. Results showed that the four compounds have little impact on the growth of a panel of 18 selected marine bacteria at a concentration of 200 µM, and up to 700 µM for some bacterial strains. Interestingly, cationic lipid BSV36 and zwitterionic lipids 3 and 4 effectively disrupt biofilm formation of Paracoccus sp. 4M6 and Vibrio sp. D02 at 200 µM and to a lesser extent of seven other bacterial strains tested. Moreover, ecotoxicological assays on four species of microalgae highlighted that compounds 3 and 4 have little impact on microalgae growth with EC50 values of 51 µM for the more sensitive species and up to 200 µM for most of the others. Amphiphilic compounds, especially zwitterionic amphiphiles 3 and 4 seem to be promising candidates against biofilm formation by marine bacteria.

Enhanced Molecular Networking Shows Microbacterium sp. V1 as a Factory of Antioxidant Proline-Rich Peptides

Two linear proline-rich peptides (1-2), bearing an N-terminal pyroglutamate, were isolated from the marine bacterium Microbacterium sp. V1, associated with the marine sponge Petrosia ficiformis, collected in the volcanic CO₂ vents in Ischia Island (South Italy). Peptide production was triggered at low temperature following the one strain many compounds (OSMAC) method. Both peptides were detected together with other peptides (3-8) via an integrated, untargeted MS/MS-based molecular networking and cheminformatic approach. The planar structure of the peptides was determined by extensive 1D and 2D NMR and HR-MS analysis, and the stereochemistry of the aminoacyl residues was inferred by Marfey's analysis. Peptides 1-8 are likely to arise from Microbacterium V1 tailor-made proteolysis of tryptone. Peptides 1 and 2 were shown to display antioxidant properties in the ferric-reducing antioxidant power (FRAP) assay.

Evaluation of DNA extraction methods and direct PCR in metabarcoding of mock and marine bacterial communities

Recent advances in new molecular biology methods and next-generation sequencing (NGS) technologies have revolutionized metabarcoding studies investigating complex microbial communities from various environments. The inevitable first step in sample preparation is DNA extraction which introduces its own set of biases and considerations. In this study, we assessed the influence of five DNA extraction methods [B1: phenol/chloroform/isoamyl extraction, B2 and B3: isopropanol and ethanol precipitations, respectively-both modifications of B1, K1: DNeasy PowerWater Kit (QIAGEN), K2: modified DNeasy PowerWater Kit (QIAGEN) and direct PCR approach (P) that completely circumvents this step on community composition and DNA yield of mock and marine sample communities from the Adriatic Sea]. B1-B3 methods generally produced higher DNA yields and more similar microbial communities, but with higher interindividual variability. Each method demonstrated significant differences in a specific community structure, where rare taxa seem to play a crucial role. There was not one superior method closest to the theoretically expected mock community composition, they all demonstrated skewed ratios, but in a similar way which might be attributed to other factors, such as primer bias or 16S rRNA gene count for specific taxa. Direct PCR represents an interesting approach when high throughput in sample processing is required. We emphasize the importance of making a cautious decision about the choice of the extraction method or direct PCR approach, but even more importantly its consistent application throughout the study.

Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria

Copper is an essential trace element for living cells. However, copper can be potentially toxic for bacterial cells when it is present in excess amounts due to its redox potential. Due to its biocidal properties, copper is prevalent in marine systems due to its use in antifouling paints and as an algaecide. Thus, marine bacteria must possess means of sensing and responding to both high copper levels and those in which it is present at only typical trace metal levels. Bacteria harbor diverse regulatory mechanisms that respond to intracellular and extracellular copper and maintain copper homeostasis in cells. This review presents an overview of the copper-associated signal transduction systems in marine bacteria, including the copper efflux systems, detoxification, and chaperone mechanisms. We performed a comparative genomics study of the copper-regulatory signal transduction system on marine bacteria to examine the influence of the environment on the presence, abundance, and diversity of copper-associated signal transduction systems across representative phyla. Comparative analyses were performed among species isolated from sources, including seawater, sediment, biofilm, and marine pathogens. Overall, we observed many putative homologs of copper-associated signal transduction systems from various copper systems across marine bacteria. While the distribution of the regulatory components is mainly influenced by phylogeny, our analyses identified several intriguing trends: (1) Bacteria isolated from sediment and biofilm displayed an increased number of homolog hits to copper-associated signal transduction systems than those from seawater. (2) A large variability exists for hits to the putative alternate σ factor CorE hits across marine bacteria. (3) Species isolated from seawater and marine pathogens harbored fewer CorE homologs than those isolated from the sediment and biofilm.

Sphingomicrobium sediminis sp. nov., isolated from marine sediment in the Republic of Korea

A Gram-stain-negative, rod-shaped, bright-orange coloured bacterium without flagellum, designated as strain GRR-S6-50^T, was isolated from a tidal flat of Garorim bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells grew aerobically at 20-37 °C (optimum, 30 °C), pH 7.0-10.0 (optimum, pH 7.0) and with 1-5 % (w/v) NaCl (optimum, 3 %). The 16S rRNA gene sequence analysis demonstrated that strain GRR-S6-50^T was closely related to Sphingomicrobium aestuariivivum AH-M8^T with a sequence similarity of 97.80 % followed by Sphingomicrobium astaxanthinifaciens CC-AMO-30B^T (97.44 %), Sphingomicrobium marinum CC- AMZ-30M^T (97.16 %), Sphingomicrobium arenosum CAU 1457^T (96.37 %), Sphingomicrobium flavum CC-AMZ-30N^T (95.31 %) and Sphingomicrobium lutaoense CC-TBT-3^T (95.23 %). The average nucleotide identity and digital DNA-DNA hybridization values with related strains ranged from 74.5 to 77.3% and 21.1 to 35.0 %, respectively. The G+C content of strain GRR-S6-50^T was 63.30 mol%. The strain has ubiquinone-10 as the predominant respiratory quinone and the major fatty acids were C_18 : 3  ω6c (54.57 %) and C_17 : 1  ω6c (10.58 %). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, three unidentified lipids and one glycolipid. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic studies, strain GRR-S6-50^T is regarded to represent a novel species within the genus Sphingomicrobium, for which the name Sphingomicrobium sediminis sp. nov. (KACC 22562^T=KCTC 92123^T=JCM 35084^T) is proposed.

"Failure To Launch": Development of a Reproductive Organ Linked to Symbiotic Bacteria

Developmental processes in animals are influenced by colonization and/or signaling from microbial symbionts. Here, we show that bacteria from the environment are linked to development of a symbiotic organ that houses a bacterial consortium in female Hawaiian bobtail squid, Euprymna scolopes. In addition to the well-characterized light organ association with the bioluminescent bacterium Vibrio fischeri, female E. scolopes house a simple bacterial community in a reproductive organ, the accessory nidamental gland (ANG). In order to understand the influences of bacteria on ANG development, squid were raised in the laboratory under conditions where exposure to environmental microorganisms was experimentally manipulated. Under conditions where hosts were exposed to depleted environmental bacteria, ANGs were completely absent or stunted, a result independent of the presence of the light organ symbiont V. fischeri. When squid were raised in the laboratory with substrate from the host's natural environment containing the native microbiota, normal ANG development was observed, and the bacterial communities were similar to wild-caught animals. Analysis of the bacterial communities from ANGs and substrates of wild-caught and laboratory-raised animals suggests that certain bacterial groups, namely, the Verrucomicrobia, are linked to ANG development. The ANG community composition was also experimentally manipulated. Squid raised with natural substrate supplemented with a specific ANG bacterial strain, Leisingera sp. JC1, had high proportions of this strain in the ANG, suggesting that once ANG development is initiated, specific strains can be introduced and subsequently colonize the organ. Overall, these data suggest that environmental bacteria are required for development of the ANG in E. scolopes. IMPORTANCE Microbiota have profound effects on animal and plant development. Hosts raised axenically or without symbionts often suffer negative outcomes resulting in developmental defects or reduced organ function. Using defined experimental conditions, we demonstrate that environmental bacteria are required for the formation of a female-specific symbiotic organ in the Hawaiian bobtail squid, Euprymna scolopes. Although nascent tissues from this organ that are involved with bacterial recruitment formed initially, the mature organ failed to develop and was absent or severely reduced in sexually mature animals that were not exposed to microbiota from the host's natural environment. This is the first example of complete organ development relying on exposure to symbiotic bacteria in an animal host. This study broadens the use of E. scolopes as a model organism for studying the influence of beneficial bacteria on animal development.

Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity

Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4'-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.

Volatiles of the Apicomplexan Alga Chromera velia and Associated Bacteria

Volatiles released by the apicomplexan alga Chromera velia CCAP1602/1 and their associated bacteria have been investigated. A metagenome analysis allowed the identification of the most abundant heterotrophic bacteria of the phycosphere, but the isolation of additional strains showed that metagenomics underestimated the complexity of the algal microbiome, However, a culture-independent approach revealed the presence of a planctomycete that likely represents a novel bacterial family. We analysed algal and bacterial volatiles by open-system-stripping analysis (OSSA) on Tenax TA desorption tubes, followed by thermodesorption, cryofocusing and GC-MS-analysis. The analyses of the alga and the abundant bacterial strains Sphingopyxis litoris A01A-101, Algihabitans albus A01A-324, "Coraliitalea coralii" A01A-333 and Litoreibacter sp. A01A-347 revealed sulfur- and nitrogen-containing compounds, ketones, alcohols, aldehydes, aromatic compounds, amides and one lactone, as well as the typical algal products, apocarotenoids. The compounds were identified by gas chromatographic retention indices, comparison of mass spectra and syntheses of reference compounds. A major algal metabolite was 3,4,4-trimethylcyclopent-2-en-1-one, an apocarotenoid indicating the presence of carotenoids related to capsanthin, not reported from algae so far. A low overlap in volatiles bouquets between C. velia and the bacteria was found, and the xenic algal culture almost exclusively released algal components.

Promising Antiparasitic Natural and Synthetic Products from Marine Invertebrates and Microorganisms

Parasitic diseases still threaten human health. At present, a number of parasites have developed drug resistance, and it is urgent to find new and effective antiparasitic drugs. As a rich source of biological compounds, marine natural products have been increasingly screened as candidates for developing new antiparasitic drugs. The literature related to the study of the antigenic animal activity of marine natural compounds from invertebrates and microorganisms was selected to summarize the research progress of marine compounds and the structure-activity relationship of these compounds in the past five years and to explore the possible sources of potential antiparasitic drugs for parasite treatment.

Time for a Change! A Spotlight on Many Neglected Facets of Sponge Microbial Biotechnology

The sponge-microorganism partnership is one of the most successful symbiotic associations exploited from a biotechnological perspective. During the last thirty years, sponge-associated bacteria have been increasingly harnessed for bioactive molecules, notably antimicrobials and cytotoxic compounds. Unfortunately, there are gaps in sponge microbial biotechnology, with a multitude of applications being understudied or ignored. In this context, the current perspective aims to shed light on these underrated facets of sponge microbial biotechnology with a balance of existent reports and proposals for further research in the field. Our overview has showcased that the members of the sponge microbiome produce biomolecules whose usage can be valuable for several economically- relevant and demanding sectors. Outside the exhaustive search for antimicrobial secondary metabolites, sponge-associated microorganisms are gifted producers of antibiofilm, antivirulence and chronic diseases-attenuating substances highly envisaged by the pharmaceutical industry. Despite still at an infant stage of research, anti-ageing enzymes and pigments of special interest for the cosmetic and cosmeceutical sectors have also been reported from the sponge microbial symbionts. In a world urging for sustainability, sponge-associated microorganisms have been proven as fruitful resources for bioremediation, including recovery of heavy-metal contaminated areas, bioleaching processes, and as bioindicators of environmental pollution. In conclusion, we propose alternatives to better assess these neglected biotechnological applications of the sponge microbiome in the hope of sparking the interest of the scientific community toward their deserved exploitation.